Table 2.
Full length TEs. Number of complete elements identified in the 12 genome assemblies. For each element type, both the total and non-redundant amount of complete elements are listed. The redundancy removal and the count of full-length Helitron copies were created following a different strategy (see Additional file 2)
| Species | LTR-R | TRIM | SINE | MULE | NA-DNAT | Helitron | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Non-Red. | Total | Non-Red. | Total | Non-Red. | Total | Non-Red. | Total | Tot. Ends | FL copies | |
| O. sativa. ssp. japonica | 3240 | 1278 | 2911 | 11 | 280 | 230 | 10468 | 172 | 77 | - | - |
| O. rufipogon | 1498 | 945 | 2724 | 11 | 276 | 197 | 10504 | 172 | - | - | - |
| O. sativa. ssp. indica | 1905 | 1253 | 3252 | 11 | 288 | 274 | 9596 | 168 | - | - | - |
| O. nivara | 1283 | 945 | 2248 | 11 | 232 | 175 | 10176 | 168 | - | - | - |
| O. glaberrima | 1520 | 865 | 2297 | 11 | 221 | 106 | 7416 | 162 | 93 | - | - |
| O. barhii | 1041 | 580 | 2384 | 11 | 244 | 206 | 9863 | 169 | - | - | - |
| O. glumipatula | 637 | 424 | 2470 | 11 | 264 | 200 | 9205 | 169 | - | - | - |
| O. longistaminata | 77 | 59 | 2344 | 11 | 344 | 293 | 5910 | 156 | - | 2279 | 338 |
| O. meridionalis | 339 | 288 | 2351 | 11 | 257 | 234 | 7316 | 162 | - | 2122 | 714 |
| O. punctata | 2906 | 2359 | 1659 | 7 | 120 | 103 | 6720 | 147 | - | 2437 | 949 |
| O. brachyantha | 395 | 360 | 1699 | 12 | 13 | 11 | 4963 | 104 | - | - | - |
| Leersia perrieri | 872 | 810 | 1624 | 6 | 116 | 110 | 3541 | 115 | - | 893 | 196 |
| Total | 15713 | 10166 | 27963 | 124 | 2655 | 2139 | 95678 | 1864 | 170 | 7731 | 2197 |